Members of the Ll transposon family (long interspersed repeat DNA or LINE family) of rats are 6.7 kb long, 5 kb of which is devoted to protein-encoding sequences (ORFs). A very strong promoter is at the left end of the element, and a guanine-rich polypurine:polypyrimidine sequence is near the right end. Although the protein-encoding sequences of mammalian Ll families are highly conserved, the promoter sequences are completely distinct. This means that novel species-specific promoter sequences have been repeatedly acquired by Ll families during mammalian evolution and that these families have been amplified repeatedly in individual mammalian species. Our recent isolation of an Ll element that is ancestral to both the present day rat and mouse Ll families and is as highly repeated in both genomes support this scenario. Our previous demonstration that the rat Ll family contains a very active promoter sequence was the first evidence that Ll DNA is not just some non-functional "junk" DNA. We have further characterized this promoter and shown that some transcripts most likely begin about 300 bp from the 51 end of the sequence, that the 650 bp promoter consists of both inhibitory and stimulatory modules which can form numerous specific DNA:protein complexes with nuclear extracts as judged by gel retardation experiments. In addition, the Ll promoter exhibits a very strong (>20-fold) synergy with the SV40 promoter sequence and can strongly activate cryptic promoters are far as 800 bp distant from it. We previously showed that the guanine-rich polypurine:polypyrimidine tract at the right end of an Ll element destabilizes contiguous duplex DNA. We now find that this tract adopts several non-B DNA structures in vitro that may explain this phenomenon. We also found that three randomly chosen Ll insertion sites adopt abnormal DNA structures as well which might facilitate targeting of Ll elements to these regions. In addition the Ll and target site non-B structures compete for supercoil energy which in vivo might modulate the supercoil-dependent properties of Ll elements and their target sites.